Natural Product: NPC607946

Natural Product IDNPC607946
Common Name
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The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 QWQGMMRHTWIOGH-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL503375
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0003467] Linear 1,3-diarylpropanoids
        • [CHEMONTID:0001630] Chalcones and dihydrochalcones
          • [CHEMONTID:0003473] 2'-Hydroxy-dihydrochalcones

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

  Chemical Representations

Standard InCHIKey QWQGMMRHTWIOGH-UHFFFAOYSA-N
Standard InCHI InChI=1S/C15H14O4/c16-11-8-13(18)15(14(19)9-11)12(17)7-6-10-4-2-1-3-5-10/h1-5,8-9,16,18-19H,6-7H2
SMILES O=C(CCc1ccccc1)c1c(O)cc(O)cc1O

  Calculated Properties

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO21410 Populus balsamifera Species Salicaceae Eukaryota Buds n.a. n.a. PMID[25927817]
NPO21807 Lindera umbellata Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[32933154]
NPO50512 Populus × berolinensis Genus Salicaceae Eukaryota n.a. n.a. n.a. PMID[38612781]
NPO21410 Populus balsamifera Species Salicaceae Eukaryota n.a. n.a. n.a. PMID[38612781]
NPO26350 Populus nigra Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21410 Populus balsamifera Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO54056 Populus deltoides Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21409 Populus angustifolia Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21807 Lindera umbellata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28202 Helichrysum tenuifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21807 Lindera umbellata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21410 Populus balsamifera Species Salicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21807 Lindera umbellata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21410 Populus balsamifera Species Salicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21807 Lindera umbellata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21410 Populus balsamifera Species Salicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21807 Lindera umbellata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26350 Populus nigra Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21409 Populus angustifolia Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21410 Populus balsamifera Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28202 Helichrysum tenuifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]

Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].



  NP Quantity Composition/Concentration

Organism ID Organism Name Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference
NPO21410 Populus balsamifera Ether extract Leaves 2.51 n.a. n.a. % PMID[38612781]
NPO50512 Populus × berolinensis Ether extract Leaves 0.57 n.a. n.a. % PMID[38612781]

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].



 Biological Activity

Molecular-level activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT100 Individual protein Glutaminase kidney isoform, mitochondrial Homo sapiens Potency n.a. 7943.3 nM PubChem BioAssay data set
NPT1255 Individual protein Sentrin-specific protease 8 Homo sapiens IC50 n.a. 100000.0 nM PubChem BioAssay data set
NPT101 Individual protein Glucagon-like peptide 1 receptor Homo sapiens Potency n.a. 28183.8 nM PubChem BioAssay data set
NPT22445 Single protein Fibroblast growth factor 22 Homo sapiens AbsAC1 > 5.0 uM PubChem BioAssay data set
NPT446 Individual protein Rap guanine nucleotide exchange factor 3 Homo sapiens Potency n.a. 100000.0 nM PubChem BioAssay data set
NPT641 Individual protein Sodium/glucose cotransporter 2 Homo sapiens IC50 = 14700.0 nM PMID[28098449]
NPT444 Individual protein Ubiquitin carboxyl-terminal hydrolase 1 Homo sapiens Potency n.a. 39810.7 nM PubChem BioAssay data set
NPT641 Individual protein Sodium/glucose cotransporter 2 Homo sapiens Inhibition n.a. n.a. % PMID[28098449]
NPT7 Individual protein Thioredoxin reductase 1, cytoplasmic Rattus norvegicus Potency n.a. 19952.6 nM PubChem BioAssay data set
NPT484 Individual protein Luciferin 4-monooxygenase Photinus pyralis Potency n.a. 37933.0 nM PubChem BioAssay data set
NPT535 Individual protein Parathyroid hormone receptor Homo sapiens Potency n.a. 25118.9 nM PubChem BioAssay data set
NPT60 Individual protein Lysosomal alpha-glucosidase Homo sapiens Potency = 39810.7 nM PubChem BioAssay data set
NPT8 Individual protein DNA polymerase iota Homo sapiens Potency n.a. 79432.8 nM PubChem BioAssay data set
NPT51 Individual protein Microtubule-associated protein tau Homo sapiens Potency = 35481.3 nM PubChem BioAssay data set
NPT442 Individual protein Ferritin light chain Equus caballus Potency = 50118.7 nM PubChem BioAssay data set
NPT640 Individual protein Sodium/glucose cotransporter 1 Homo sapiens IC50 = 7900.0 nM PMID[28098449]
NPT640 Individual protein Sodium/glucose cotransporter 1 Homo sapiens Inhibition n.a. n.a. % PMID[28098449]
NPT532 Individual protein Lysine-specific demethylase 4A Homo sapiens Potency n.a. 89125.1 nM PubChem BioAssay data set

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT169 Cell line B16-F10 Mus musculus IC50 = 218950.0 nM PMID[27720556]
NPT71 Cell line HEK293 Homo sapiens Activity n.a. n.a. n.a. PMID[28098449]
NPT169 Cell line B16-F10 Mus musculus Inhibition = 25.0 % PMID[27720556]
NPT169 Cell line B16-F10 Mus musculus Inhibition > 50.0 % PMID[27720556]
NPT28438 Unchecked Unchecked n.a. IC50 = 68480.0 nM PMID[27720556]
NPT28438 Unchecked Unchecked n.a. Inhibition n.a. n.a. % PMID[28098449]
NPT28438 Unchecked Unchecked n.a. Potency = 29092.9 nM PubChem BioAssay data set
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity = 0.0 % PMID[521818]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity = 100.0 % PMID[521818]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference





 Experimental ADME

Experiment Model Experiment Tissue ADME Type ADME Relation ADME Value ADME Unit Reference





 Experimental Toxicity

Quantitative toxicity

Experiment Model Experiment Organism Toxicity Type Toxicity Relation Toxicity Value Toxicity Unit Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption
Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]


  Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

●  The left chart: Distribution of similarity level between NPC607946 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.5 or Top200).

Similarity Score Similarity Level Natural Product ID
0.7838 Intermediate Similarity NPC242895
0.7436 Intermediate Similarity NPC179494
0.7073 Intermediate Similarity NPC604715
0.7 Intermediate Similarity NPC156139
0.7 Intermediate Similarity NPC233056
0.6829 Remote Similarity NPC294593
0.625 Remote Similarity NPC608363
0.5778 Remote Similarity NPC275504
0.5778 Remote Similarity NPC485643
0.5714 Remote Similarity NPC133909
0.5676 Remote Similarity NPC12936
0.5625 Remote Similarity NPC194949
0.5556 Remote Similarity NPC82225
0.5532 Remote Similarity NPC28753
0.5455 Remote Similarity NPC204960
0.5333 Remote Similarity NPC195262
0.5179 Remote Similarity NPC600314
0.5128 Remote Similarity NPC146642
0.5122 Remote Similarity NPC149246
0.5106 Remote Similarity NPC188814
0.5106 Remote Similarity NPC608141
0.5102 Remote Similarity NPC20560

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC607946 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
NPD

Bioactivity similarity

  Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.
Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data